Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Docker-in-Docker (DinD) capabilities of public runners deactivated.
More info
Open sidebar
VEBER Philippe
codepi
Commits
bbdd8e37
Commit
bbdd8e37
authored
Nov 17, 2020
by
Philippe Veber
Browse files
Simulation_dataset: separate in-house simulation and bppseqgen's
parent
265897c0
Changes
2
Expand all
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
585 additions
and
454 deletions
+585
-454
lib/simulation_dataset.ml
lib/simulation_dataset.ml
+515
-374
lib/simulation_dataset.mli
lib/simulation_dataset.mli
+70
-80
No files found.
lib/simulation_dataset.ml
View file @
bbdd8e37
This diff is collapsed.
Click to expand it.
lib/simulation_dataset.mli
View file @
bbdd8e37
...
...
@@ -9,52 +9,18 @@ type tree =
branch_length2
:
float
;
}
type
'
s
benchmark
=
{
method_labels
:
string
list
;
method_outputs
:
float
option
array
list
;
average_precision
:
(
float
*
(
float
*
float
))
list
;
site_model
:
'
s
array
;
ancestral_counts
:
int
Phylogenetics
.
Amino_acid
.
table
array
;
convergent_counts
:
int
Phylogenetics
.
Amino_acid
.
table
array
;
}
module
type
S
=
sig
type
t
type
site_model
type
query
include
Detection_pipeline
.
Query
with
type
t
:=
t
include
Detection_pipeline
.
S
with
type
query
:=
t
include
Detection_pipeline
.
S
with
type
query
:=
query
val
alignment_plot
:
t
->
svg
file
val
benchmark
:
t
->
text
file
list
->
site_model
benchmark
workflow
val
rds_of_benchmark
:
site_model
benchmark
workflow
->
rds
file
val
alignment_plot
:
query
->
svg
file
end
type
t
val
bppseqgen_mixed
:
?
ne_s
:
float
->
?
seed
:
int
->
tree
:
tree
->
profiles
:
string
->
n_h0
:
int
->
n_ha
:
int
->
unit
->
t
val
bppseqgen
:
hyp
:
Convergence_hypothesis
.
t
->
tree
:
tree
->
profiles
:
string
->
nb_sites
:
int
->
seed
:
int
->
t
module
Mutsel_param
:
sig
type
t
val
make
:
module
Mutsel
:
sig
include
S
val
query
:
?
branch_scale
:
float
->
?
ne_s
:
float
*
float
->
?
gBGC
:
float
*
float
->
...
...
@@ -64,62 +30,86 @@ module Mutsel_param : sig
n_h0
:
int
->
n_ha
:
int
->
unit
->
t
query
val
simulation
:
t
->
query
->
Codepitk
.
Simulator
.
Site_independent_mutsel
.
simulation
workflow
end
val
mutsel
:
?
branch_scale
:
float
->
?
ne_s
:
float
*
float
->
?
gBGC
:
float
*
float
->
?
seed
:
int
->
tree
:
tree
->
profiles
:
string
->
n_h0
:
int
->
n_ha
:
int
->
unit
->
t
val
of_mutsel_param
:
Mutsel_param
.
t
->
t
type
benchmark
=
{
method_labels
:
string
list
;
method_outputs
:
float
option
array
list
;
average_precision
:
(
float
*
(
float
*
float
))
list
;
site_model
:
[
`Convergent
|
`Non_convergent
]
array
;
ancestral_counts
:
int
Phylogenetics
.
Amino_acid
.
table
array
;
convergent_counts
:
int
Phylogenetics
.
Amino_acid
.
table
array
;
}
include
Detection_pipeline
.
Query
with
type
t
:=
t
include
Detection_pipeline
.
S
with
type
query
:=
t
val
benchmark_statistics
:
Codepitk
.
Simulator
.
Site_independent_mutsel
.
simulation
workflow
->
labels
:
string
list
->
results
:
(
text
file
*
int
)
list
->
binary_file
file
val
oracle
:
t
->
text
file
(* val benchmark : t -> (t -> text file) list -> benchmark workflow
*
* val rds_of_benchmark : benchmark workflow -> rds file *)
val
alignment_plot
:
t
->
svg
file
(** stuff for gbgc SBME paper *)
type
gBGC_t
=
|
Global
of
float
|
Convergent
of
float
*
float
val
multinomial_benchmark
:
t
->
pdf
file
type
param_t
val
benchmark
:
?
mode
:
[
`fast
|
`full
]
->
t
->
svg
file
val
explore_params
:
f
:
(
param_t
->
'
a
)
->
((
float
*
gBGC_t
)
*
'
a
)
list
val
benchmark2
:
t
->
pdf
file
val
simu_of_param
:
?
n_h0
:
int
->
param_t
->
query
val
benchmark_statistics
:
Codepitk
.
Simulator
.
Site_independent_mutsel
.
simulation
workflow
->
labels
:
string
list
->
results
:
(
text
file
*
int
)
list
->
binary_file
file
val
filter_results
:
f
:
(
'
a
->
bool
)
->
(
param_t
*
'
a
)
list
->
(
param_t
*
'
a
)
list
(** stuff for gbgc SBME paper *)
type
gBGC_t
=
|
Global
of
float
|
Convergent
of
float
*
float
type
record_t
type
param_t
val
record_of_simu
:
query
->
record_t
workflow
val
explore_params
:
f
:
(
param_t
->
'
a
)
->
((
float
*
gBGC_t
)
*
'
a
)
list
val
realistic_result
:
record_t
->
bool
end
val
simu_of_param
:
?
n_h0
:
int
->
param_t
->
t
module
Bppseqgen
:
sig
type
t
val
filter_results
:
f
:
(
'
a
->
bool
)
->
(
param_t
*
'
a
)
list
->
(
param_t
*
'
a
)
list
val
bppseqgen_mixed
:
?
ne_s
:
float
->
?
seed
:
int
->
tree
:
tree
->
profiles
:
string
->
n_h0
:
int
->
n_ha
:
int
->
unit
->
t
val
bppseqgen
:
hyp
:
Convergence_hypothesis
.
t
->
tree
:
tree
->
profiles
:
string
->
nb_sites
:
int
->
seed
:
int
->
t
type
record_t
include
Detection_pipeline
.
Query
with
type
t
:=
t
include
Detection_pipeline
.
S
with
type
query
:=
t
val
oracle
:
t
->
text
file
val
record_of_simu
:
t
->
record_t
workflow
val
alignment_plot
:
t
->
svg
file
val
multinomial_benchmark
:
t
->
pdf
file
val
realistic_result
:
record_t
->
bool
val
benchmark
:
?
mode
:
[
`fast
|
`full
]
->
t
->
svg
file
val
benchmark2
:
t
->
pdf
file
end
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment